I have just finished with the game personally and it is one of those games where you get to the end credits and think..wow.. that was amazing. Then you spend the rest of the credit roll time pondering about the story and figuring out the intricacies.
The bit you seem to be getting stuck at is sort of like the intro, it heats up fast after that section, so keep pressing on for a bit and trust me.. you will enjoy it
It is a masterpiece. Play it.



